is_paired_end: Guess whether the samples are paired end

In LieberInstitute/recount3: Explore and download data from the recount3 project

Guess whether the samples are paired end

Description

Based on two alignment metrics, this function guesses the samples are paired end or not.

Usage

is_paired_end(
  x,
  avg_mapped_read_length = "recount_qc.star.average_mapped_length",
  avg_read_length = "recount_seq_qc.avg_len"
)

Arguments

x	Either a RangedSummarizedExperiment-class created by create_rse() or the sample metadata created by read_metadata().
avg_mapped_read_length	A character(1) specifying the metdata column name that contains the average fragment length after aligning. This is typically twice the average read length for paired-end reads.
avg_read_length	A character(1) specifying the metadata column name that contains the average read length prior to aligning.

Value

A logical() vector specifying whether each sample was likely paired-end or not.

See Also

Other count transformation functions: compute_read_counts(), compute_scale_factors(), transform_counts()

Examples

## Download the metadata for SRP009615, a single-end study
SRP009615_meta <- read_metadata(
    metadata_files = file_retrieve(
        locate_url(
            "SRP009615",
            "data_sources/sra",
        )
    )
)

## Are the samples paired end?
is_paired_end(SRP009615_meta)

## Download the metadata for DRP000499, a paired-end study
DRP000499_meta <- read_metadata(
    metadata_files = file_retrieve(
        locate_url(
            "DRP000499",
            "data_sources/sra",
        )
    )
)
is_paired_end(DRP000499_meta)

LieberInstitute/recount3 documentation built on May 10, 2023, 6:01 a.m.